how to update the patch files.

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Hi guys,
I have question about patches.
I have source tree and I have develop my own patch changing few files from the source tree.
Now new version of the source tree arives and I want to apply my own old patches on the new source tree.
Some of the files I am patching however are changed in the new source tree release.
I can fix my patches manually but I think there should be a tool that get 3 files: old_source_file, new_source_file, patch_for_the_old_source_file and produce patch_for_the_new_source_file as result.
Can you please give me a clue?
I am using unified diff to create my patches. I know that often my old patches will apply with some offset over the new source files but still I think that the process I am requesting makes sence.
What do you think?
And Marry Cristmas
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I have a huge and wide tree of subdirectories, tree A. Inside the tree are obsolete files. These files I have in another, smaller tree (which contains only the obsolete files), tree B. I now need a script that deletes in tree A every occurrence of a file in tree B (based only on filenames, not the content).